The structural basis for peptide selection by the transport receptor OppA

Abstract

Oligopeptide-binding protein A (OppA) from Lactococcus lactis binds peptides of an exceptionally wide range of lengths (4-35 residues), with no apparent sequence preference. Here, we present the crystal structures of OppA in the open-and closed-liganded conformations. The structures directly explain the protein's phenomenal promiscuity. A huge cavity allows binding of very long peptides, and a lack of constraints for the position of the N and C termini of the ligand is compatible with binding of peptides with varying lengths. Unexpectedly, the peptide's amino-acid composition (but not the exact sequence) appears to have a function in selection, with a preference for proline-rich peptides containing at least one isoleucine. These properties can be related to the physiology of the organism: L. lactis is auxotrophic for branched chain amino acids and favours proline-rich caseins as a source of amino acids. We propose a new mechanism for peptide selection based on amino-acid composition rather than sequence.

Structure and Mode of Peptide Binding of Pheromone Receptor PrgZ

“…However, for high-affinity binding of a given peptide, the physicochemical properties of the side chains (size and hydrophobicity) should match those of the PrgZ pockets. Further support for this notion comes from the observation that water molecules reside in all side chain pockets, and these could form bridging hydrogen bonds to bound peptides, as seen previously in OppA (14,15,29). The more hydrophilic pockets harbor more defined water molecules inside compared with the more hydrophobic ones (Table 2).…”

“…The volume of the binding cavity of PrgZ* is 1600 Å 3 , which is smaller than that of AppA from Bacillus subtilis (2500 Å 3 ) or OppA from L. lactis (4900 Å 3 ) but larger than that of OppA from S. typhimurium (1000 Å 3 ) (14). The side chains of cCF10 are located in defined, mostly hydrophobic, side chain pockets, and with the exception of a hydrogen bond to the Thr-3 side chain, the side chains do not form specific interactions with the protein.…”

“…PrgZ has an extra domain, as has been previously described for OppA from S. typhimurium and L. lactis (14,29), and thus has a total of three domains (domains I-III). Substrate-binding proteins are structurally related even though their sequence identity is often below 20% (30).…”

“…It is clear that iCF10 and cCF10 compete for the same binding site in PrgX, but it has not been shown to date whether iCF10 also competes with cCF10 for binding to PrgZ. Furthermore, it is unknown what discriminates PrgZ from OppA in terms of structure determinants that allow the pheromone receptor to bind cCF10 with high affinity, whereas OppA, based on studies of its homologs in Salmonella typhimurium, Escherichia coli, and Lactococcus lactis, is highly promiscuous and binds a wide variety of peptides with moderate affinity (13)(14)(15). To gain detailed insight in how PrgZ binds its ligands, we present here the structure of PrgZ complexed with cCF10, as well as ligand-binding studies.…”

Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts

“…4C). This absence of side chains is a consequence of the conformational ensembles of multiple ligands and is typical for a mixture of endogenous peptides, as seen before in other examples of peptide-binding proteins (42). We have crystallized a trapped uncleaved peptide ensemble likely similar to the initial peptide-binding intermediate in the wild-type enzyme.…”